Roles of solvent accessibility and gene expression in modeling protein sequence evolution

Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2

Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.

Development of Microsatellite Markers for a Dioecious Herpetospermum pedunculosum (Cucurbitaceae)

Understanding the evolution of flower diversity is a central topic in plant evolutionary ecology, and natural selection on floral traits via male fitness could be estimated quantitatively using microsatellites. Here, based on RNA sequencing, we developed simple sequence repeat primers and verified polymorphisms in 2 wild populations of Herpetospermum pedunculosum (Cucurbitaceae), a dioecious annual plants native to the Himalaya Mountains. A total of 131 paired primers were designed; 15 paired primers were found to be polymorphic, with the expected heterozygosity varying between 0.280 and 0.767. We also identified 58 genotypes in 20 plants from the 2 populations. Conclusively, these primers could be effective in examining male fitness and population genetic structure of H pedunculosum in future studies.

Transcriptome Analysis and Microsatellite Markers Development of a Traditional Chinese Medicinal Herb Halenia elliptica D. Don (Gentianaceae)

Halenia elliptica is a popular Chinese medicinal herb that is used to treat jaundice disease and virus hepatitis, and its wild populations have been reduced significantly due to overharvesting recently. However, effective conservation could not be implemented because of the lack of genomic information and genetic markers. In this study, a de novo transcriptome of H elliptica was sequenced using the NGS Illumina, and 132 695 unigenes with the length >200 bp (base pairs) were obtained. Among them, a total of 32 109 unigenes were scanned to develop simple sequence repeats (SSRs). Based on NCBI (National Center for Biotechnology Information) nonredundant database (Nr), these SSR sequences were annotated and assigned into gene ontology categories. In addition, we designed 126 pairs of SSR primers for polymerase chain reaction amplification, of which 12 pairs were identified to be polymorphic among 40 individuals from 8 populations. We then used the 12 polymorphic SSRs to construct a UPGMA dendrogram of the 40 individuals. In addition, a significant correlation between the genetic relationship and the geographic distance was found, suggesting a phylogeographic structure in H elliptica. Moreover, 2 of these SSRs were also successfully amplified in a related species Veratrilla baillonii, suggesting their cross-species transferability. Generally, the SSR markers with high polymorphisms identified in this study provide valuable genetic resources and represent an initial step for exploring the genetic diversity and population histories of H elliptica and its related species.

Deep sequencing and transcriptome analyses to identify genes involved in secoiridoid biosynthesis in the Tibetan medicinal plant Swertia mussotii

Swertia mussotii Franch. is an important traditional Tibetan medicinal plant with pharmacological properties effective in the treatment of various ailments including hepatitis. Secoiridoids are the major bioactive compounds in S. mussotii. To better understand the secoiridoid biosynthesis pathway, we generated transcriptome sequences from the root, leaf, stem, and flower tissues, and performed de novo sequence assembly, yielding 98,613 unique transcripts with an N50 of 1,085 bp. Putative functions could be assigned to 35,029 transcripts (35.52%) based on BLAST searches against annotation databases including GO and KEGG. The expression profiles of 39 candidate transcripts encoding the key enzymes for secoiridoid biosynthesis were examined in different S. mussotii tissues, validated by qRT-PCR, and compared with the homologous genes from S. japonica, a species in the same family, unveiling the gene expression, regulation, and conservation of the pathway. The examination of the accumulated levels of three bioactive compounds, sweroside, swertiamarin, and gentiopicroside, revealed their considerable variations in different tissues, with no significant correlation with the expression profiles of key genes in the pathway, suggesting complex biological behaviours in the coordination of metabolite biosynthesis and accumulation. The genomic dataset and analyses presented here lay the foundation for further research on this important medicinal plant.